Add InstaNovo and InstaNovo+ import support

[BioGeek]

InstaNovo is a de novo peptide sequencing tool.

This PR adds support for normalized CSV output from InstaNovo v1.2.2 in three modes:

• InstaNovo: de novo peptide sequencing with the transformer-based InstaNovo model.
• InstaNovo+: de novo peptide sequencing with the diffusion-based InstaNovo+ model.
• InstaNovo with refinement: InstaNovo predictions refined with InstaNovo+.

This PR forms the basis for a bunch of related PRs within the CompOmics ecosystem.

Changes

• Adds built-in advocates for:
  • InstaNovo
  • InstaNovo+
  • InstaNovo with refinement
• Adds identification-file readers for:
  • .instanovo.csv
  • .instanovoplus.csv
  • .instanovo.refined.csv
• Adds support for normalized InstaNovo v1.2.2 CSV columns.
• Adds support for the default UniMod annotations emitted by InstaNovo's default residue configuration.
• Adds sample-row based tests for InstaNovo, InstaNovo+, and refined output.
• Improves spectrum-title matching for real MGF/mzML titles.
• Handles whitespace-padded precursor charges and skips rows with invalid charges.
• Adds shared InstaNovo parameter classes used by SearchGUI advanced settings.

Supporting Fixes

Shared fixes needed for the InstaNovo de novo end-to-end flow (SearchGUI → PeptideShaker):

• Declares the ThermoRawFileParser mzML output ending as .mzML (the canonical extension the tool writes) so converted spectra are found on case-sensitive file systems.
• Aligns log4j-api to 2.25.4 to match the bumped log4j-core, fixing a runtime NoSuchFieldError.
• Suppresses (logs but does not pop a dialog for) the benign Nimbus look-and-feel ClassCastException (ColorUIResource cannot be cast to Boolean) thrown while building chart popup menus on recent JDKs.

Implementation Notes

• The refined workflow is represented separately from standalone InstaNovo+ so downstream tools can distinguish both result types.
• Refined output reports software metadata for the refined workflow and the underlying InstaNovo/InstaNovo+ tools.
• Spectrum title lookup is cached per spectrum file during CSV import.

Tests

Ran:

mvn -Dtest=com.compomics.util.test.experiment.io.identifications.TestInstaNovoIdfileReader,com.compomics.util.test.parameters.identification.tool_specific.TestInstaNovoParameters test
mvn -DskipTests -Dmaven.javadoc.skip=true install

Covered by tests:

• InstaNovo v1.2.2 CSV parsing.
• InstaNovo+ v1.2.2 CSV parsing.
• InstaNovo with refinement v1.2.2 CSV parsing.
• default InstaNovo UniMod modification mapping.
• realistic non-numeric spectrum titles with scan= tokens.
• invalid and whitespace-padded precursor charges.

Merge Order

Recommended order:

1. This PR
2. Add SearchGUI support for InstaNovo and InstaNovo+ searchgui#387
3. Add PeptideShaker import UI support for InstaNovo result files peptide-shaker#570
4. Add DeNovoGUI compatibility APIs to Utilities #74
5. Add InstaNovo support to DeNovoGUI denovogui#53
6. Update SearchGUI recipe to 4.3.17 bioconda/bioconda-recipes#66604
7. Update PeptideShaker recipe to 3.0.13 bioconda/bioconda-recipes#66603
8. Expose InstaNovo workflows in online input form barsnes-group/peptide-shaker-online#30
9. Bump PeptideShaker wrappers for InstaNovo support galaxyproteomics/tools-galaxyp#828